I have been using a portable USB disc for storing media. After several weeks of inactivity, when I used it with git-annex again I noticed it was running very slowly. I mean, it is an USB 2.0 connection, git-annex sync would take a few minutes, but now it takes many hours.

When adding files to it (git-annex add), I would see the list of files passing by at the speed I would expect, but then, at the end, I would have to wait; the next day I saw the operation had completed. git-annex status makes me wait a similar amount of time, and git-annex sync also makes me wait, even when it has nothing to do — I saw top reporting 100% CPU usage, iotop saying git and fuse were saturating the USB connection to its maximum.

File operations outside of git-annex seem to work fine, so I can't blame the hardware or the filesystem (NTFS mounted with fuse).

I would like to know your thought about this problem, that I was not noticing before. Here is the regular information to help you form an oppinion:

% time git annex status --debug
[2016-09-07 20:20:46.093990203] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","-c","core.bare=false","status","-uall","-z"]
[2016-09-08 15:05:23.239573491] chat: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","-c","core.bare=false","cat-file","--batch"]
[2016-09-08 15:08:25.605689622] process done ExitSuccess
git annex status --debug  33802.97s user 1162.38s system 51% cpu 18:47:39.54 total

% git-annex info
repository mode: direct
trusted repositories: 0
semitrusted repositories: 4
    00000000-0000-0000-0000-000000000001 -- web
    00000000-0000-0000-0000-000000000002 -- bittorrent
    069de9a2-dc53-4c0a-82e0-a61a1f29e6b3 -- stratos PC [stratos]
    49b5b3a4-56ac-4cf2-aed9-1c23d3181c97 -- Toshiba USB HDD [here]
untrusted repositories: 0
transfers in progress: none
available local disk space: 120.41 gigabytes (+1 megabyte reserved)
local annex keys: 6303
local annex size: 1.87 terabytes
annexed files in working tree: 7412
size of annexed files in working tree: 2.24 terabytes
bloom filter size: 32 mebibytes (1.3% full)
backend usage: 
    SHA256E: 7412

% git-annex version
git-annex version: 6.20160613-g1e4e6f4
build flags: Assistant Webapp Pairing Testsuite S3(multipartupload)(storageclasses) WebDAV Inotify DBus DesktopNotify XMPP ConcurrentOutput TorrentParser MagicMime Feeds Quvi
key/value backends: SHA256E SHA256 SHA512E SHA512 SHA224E SHA224 SHA384E SHA384 SHA3_256E SHA3_256 SHA3_512E SHA3_512 SHA3_224E SHA3_224 SHA3_384E SHA3_384 SKEIN256E SKEIN256 SKEIN512E SKEIN512 SHA1E SHA1 MD5E MD5 WORM URL
remote types: git gcrypt S3 bup directory rsync web bittorrent webdav tahoe glacier ddar hook external
local repository version: 5
supported repository versions: 5 6
upgrade supported from repository versions: 0 1 2 3 4 5
operating system: linux x86_64

Thank you for your time.